qb.scanone              package:qtlbim              R Documentation

_G_e_n_o_m_e _S_c_a_n _f_o_r _M_a_i_n _L_o_c_i _I_n_v_o_l_v_e_d _i_n _P_h_e_n_o_t_y_p_i_c _T_r_a_i_t

_D_e_s_c_r_i_p_t_i_o_n:

     This method extracts iteration diagnostics and mainloci from the
     'qb' object and returns a data frame (of class 'qb.scanone')
     containing information on environmental variance, explained
     variance components, non-epistatic variance components.

_U_s_a_g_e:

     qb.scanone(qbObject, epistasis = TRUE, scan, type, covar, adjust.covar,
       chr, sum.scan = "yes", min.iter = 1,
       aggregate = TRUE, half = FALSE, verbose = FALSE)

_A_r_g_u_m_e_n_t_s:

qbObject: An object of class 'qb'.

epistasis: If 'TRUE' then information about epistasis is included.

    scan: Vector of diagnostics to scan (see below).

    type: Type of scan; default is "heritability" (see below).

   covar: Covariate(s) to include; default is 'seq(nfixcov)' where
          'nfixcov' is taken from 'qb.data'. Set to 0 to exclude any
          covariates.

adjust.covar: Adjustments to covariates. Default is 'NA', which adjusts
          by covariate mean values. Values are assumed to be in order
          of fixed covariates.

     chr: Chromosomes to subset on if not 'NULL'.

sum.scan: Sum over 'scan' diagnostics if "yes" or "only"; only report
          'sum' if "only".

min.iter: Include only samples at loci if minimum number of iterations
          is at least 'min.iter'; default is to include all ('min.iter'
          = 1).

aggregate: Aggregate effects into main, epis, gbye if 'TRUE'.

    half: Cut epistatic effects in half if 'TRUE'.

 verbose: Give verbose feedback if 'TRUE'.

_D_e_t_a_i_l_s:

     The 'type' specifies what type of scan is performed. Scan produces
     marginal estimates of diagnostics at each potential loci across
     the genome. That is, values are adjusted for other possible QTL
     simply by taking the marginal average over MCMC samples. Choices
     of 'type' are "heritability", "LPD", "LR", "deviance",
     "detection", "variance", "estimate", "cellmean", "count", "log10",
     "posterior", "logposterior" (i.e. log10(posterior)), "BF",
     "2logBF" (i.e. 2*ln(BF)), and "nqtl" (number of linked QTL).
     Default is "LPD".

     Type "heritability" is actually R-squared at this point, not the
     theoretical heritability. Types "LPD", "LR" and "deviance" are all
     proportional to each other in the usual sense; "LPD" is computed
     to agree with 'lod' from 'scanone' if models were restricted to
     one QTL and missing genotypes are imputed. Detection is the
     marginal posterior probability of detectio of a QTL at a locus.
     Types "variance" and "estimate" yield, respectively, the marginal
     variance components and the marginal parameter estimates at each
     loci. Type "cellmean" gives marginal estimates for A, H, B
     genotypes (these are single character codes for AA, AB, BB,
     respectively). The remaining count types provide diagnostics.
     Types "count" and "log10" report on number of MCMC samples in raw
     or logged scale. Type  "posterior" ("logposterior") yields the
     marginal (log) posterior probability. Type "BF" ("2logBF") gives
     the marginal Bayes factor per loci; both are proportional to
     "count". Type "nqtl" gives the average number of linked loci,
     which can be useful in sorting out multiple linked loci.

     The 'scan' specifies the model effects to include for all types
     except the counts. Aggregated effects (default except for type
     "cellmean") are "main", "epistasis" and "GxE" (genotype by
     environment). Individual model effects can be requested  as "add",
     "dom", "aa", "ad", "da", "dd". In addition, GxE terms, if present
     are included automatically if 'covar' is not 0. For type
     "estimate", main effects for "add" and "dom" are adjusted for any
     covariate GxE effects. The 'sum.scan' is used for all types but
     the counts to get a summary across 'scan' effects.

_V_a_l_u_e:

     Returns an object of class 'qb.scanone' (a data frame) containing
     effects selected according to 'type' and 'scan'.

_A_u_t_h_o_r(_s):

     Brian S. Yandell, yandell@stat.wisc.edu

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.qtlbim.org>

_S_e_e _A_l_s_o:

     'summary.qb.scanone', 'plot.qb.scanone'

_E_x_a_m_p_l_e_s:

     temp <- qb.scanone(qbExample)
     summary(temp)
     plot(temp)

